There have been quite a few new systems found since the outbreak of the Derra virus.. none of them have resulted in revealing a hidden race. Are there still hidden races out there? If so.. I guess they have not been discovered because they are so rare? I thought someone would have stumbled across one by now...

THey should be in their canon position, or as near as the ASims can do it. That would be one of the reasons why the hidden races haven't been named as it would give people a massive advantage in finding them. I think it speaks for the team that dealt with adding them that so far only one race has been found.

Are hidden systems added to systems that are completely empty or do could they be added to a deep space location that already has stations?

And if they would be added to locations that might already have stations, what would happen if the sun is planned for where the stations are. Similarly to black holes. Would the system be redesigned or how are they placed? (If that's not restricted info)

Systems can appear where stations etc are now. As for how it deals with it, from teh galaxy shift and some issues we had there, those entities would still exist just in a deep space layer. It would show as being in that place but would be unavailable until an admin teleported back into its correct position. I would presume that is how it would still work, unless the devs have made a workaround to avoid it.